Analysis of MCF10A in 16 different conditions 2 biological replicates per sample
| x | |
|---|---|
| GM_none_1 | 1.0363804 |
| IM_none_1 | 0.8394101 |
| IM_none_2 | 1.0312687 |
| IM_none_Glut_1 | 0.9116712 |
| IM_none_Glut_2 | 1.0200687 |
| IM_none_EGF_1 | 0.6409089 |
| IM_none_EGF_2 | 1.0285384 |
| IM_none_noIns_1 | 0.9494883 |
| IM_none_noIns_2 | 1.0222049 |
| IM_none_noGluc_1 | 1.0654041 |
| IM_none_noGluc_2 | 0.8620713 |
| IM_none_noHC_1 | 1.1827572 |
| IM_none_noHC_2 | 1.0060447 |
| IM_none_noCT_1 | 1.0396167 |
| IM_none_noCT_2 | 1.0252612 |
| IM_none_AMPKact_1 | 1.0266369 |
| IM_none_AMPKact_2 | 1.1027958 |
| IM_none_AKTinhib_1 | 1.0720796 |
| IM_none_AKTinhib_2 | 1.1338035 |
| IM_none_ERKinhib_1 | 1.0241596 |
| IM_none_ERKinhib_2 | 1.1516436 |
| IM_none_mTORC1inhib_1 | 1.0075421 |
| IM_none_mTORC1inhib_2 | 1.1921120 |
| IM_none_Oligo_1 | 0.6264784 |
| IM_none_Oligo_2 | 1.0106023 |
| IM_none_MPCinhib_1 | 1.1699916 |
| IM_none_MPCinhib_2 | 0.9356112 |
| IM_none_LDHinhib_1 | 1.0862708 |
| IM_none_LDHinhib_2 | 1.0147222 |
| IM_none_IL6_1 | 1.1514910 |
| IM_none_IL6_2 | 1.0673677 |
Removal of - Oligomycin - EGF positive - Growth medium - IL6 - IM HC neg - IM ins neg
I think we can see a pretty evident batch effect per replicate!
I think we can see a pretty evident batch effect per replicate!
Same thing here, the batch effect can seen and disappears with the limma::removeBatchEffect function. Meaning I need to include replicates in the design formula.
| x |
|---|
| Intercept |
| condition_AKT_inhibitor_vs_IM |
| condition_AMPK_activator_vs_IM |
| condition_ERK_inhibitor_vs_IM |
| condition_Growth_Medium_vs_IM |
| condition_IL6_vs_IM |
| condition_IM_CT_neg_vs_IM |
| condition_IM_EGF_pos_vs_IM |
| condition_IM_Glucose_neg_vs_IM |
| condition_IM_Glutamine_pos_vs_IM |
| condition_IM_HC_neg_vs_IM |
| condition_IM_Ins_neg_vs_IM |
| condition_LDH_inhibitor_vs_IM |
| condition_MPC_inhibitor_vs_IM |
| condition_mTORC1_inhibitor_vs_IM |
| condition_Oligomycin_vs_IM |
| replicate |
Maybe - Oligomycin vs IM - EGF vs IM - EGF vs Oligomycin
| x |
|---|
| Intercept |
| condition_IM_vs_IM_EGF_pos |
| condition_AKT_inhibitor_vs_IM_EGF_pos |
| condition_AMPK_activator_vs_IM_EGF_pos |
| condition_ERK_inhibitor_vs_IM_EGF_pos |
| condition_Growth_Medium_vs_IM_EGF_pos |
| condition_IL6_vs_IM_EGF_pos |
| condition_IM_CT_neg_vs_IM_EGF_pos |
| condition_IM_Glucose_neg_vs_IM_EGF_pos |
| condition_IM_Glutamine_pos_vs_IM_EGF_pos |
| condition_IM_HC_neg_vs_IM_EGF_pos |
| condition_IM_Ins_neg_vs_IM_EGF_pos |
| condition_LDH_inhibitor_vs_IM_EGF_pos |
| condition_MPC_inhibitor_vs_IM_EGF_pos |
| condition_mTORC1_inhibitor_vs_IM_EGF_pos |
| condition_Oligomycin_vs_IM_EGF_pos |
| replicate |
## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] clusterProfiler_4.6.0 msigdbr_7.5.1
## [3] xlsx_0.6.5 pheatmap_1.0.12
## [5] ggrepel_0.9.2 biomaRt_2.54.1
## [7] cowplot_1.1.1 DESeq2_1.38.1
## [9] SummarizedExperiment_1.28.0 Biobase_2.58.0
## [11] MatrixGenerics_1.10.0 matrixStats_0.62.0
## [13] GenomicRanges_1.49.0 GenomeInfoDb_1.34.4
## [15] IRanges_2.32.0 S4Vectors_0.36.0
## [17] BiocGenerics_0.44.0 forcats_0.5.2
## [19] stringr_1.4.1 dplyr_1.0.10
## [21] purrr_0.3.5 readr_2.1.3
## [23] tidyr_1.2.1 tibble_3.1.8
## [25] ggplot2_3.4.0 tidyverse_1.3.2
## [27] RColorBrewer_1.1-3
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.2 tidyselect_1.2.0 RSQLite_2.2.19
## [4] AnnotationDbi_1.60.0 grid_4.2.2 BiocParallel_1.32.4
## [7] scatterpie_0.1.8 munsell_0.5.0 codetools_0.2-18
## [10] ragg_1.2.5 withr_2.5.0 colorspace_2.0-3
## [13] GOSemSim_2.24.0 filelock_1.0.2 highr_0.9
## [16] knitr_1.41 rstudioapi_0.14 rJava_1.0-6
## [19] DOSE_3.24.2 labeling_0.4.2 GenomeInfoDbData_1.2.9
## [22] polyclip_1.10-4 bit64_4.0.5 farver_2.1.1
## [25] downloader_0.4 vctrs_0.5.0 treeio_1.22.0
## [28] generics_0.1.3 gson_0.0.9 xfun_0.34
## [31] timechange_0.1.1 BiocFileCache_2.6.1 R6_2.5.1
## [34] graphlayouts_0.8.4 locfit_1.5-9.6 bitops_1.0-7
## [37] cachem_1.0.6 fgsea_1.24.0 gridGraphics_0.5-1
## [40] DelayedArray_0.23.2 assertthat_0.2.1 scales_1.2.1
## [43] ggraph_2.1.0 enrichplot_1.18.3 googlesheets4_1.0.1
## [46] gtable_0.3.1 tidygraph_1.2.2 rlang_1.0.6
## [49] systemfonts_1.0.4 splines_4.2.2 lazyeval_0.2.2
## [52] gargle_1.2.1 broom_1.0.1 yaml_2.3.6
## [55] reshape2_1.4.4 modelr_0.1.10 backports_1.4.1
## [58] qvalue_2.30.0 tools_4.2.2 ggplotify_0.1.0
## [61] ellipsis_0.3.2 jquerylib_0.1.4 Rcpp_1.0.9
## [64] plyr_1.8.8 progress_1.2.2 zlibbioc_1.44.0
## [67] RCurl_1.98-1.9 prettyunits_1.1.1 viridis_0.6.2
## [70] haven_2.5.2 fs_1.5.2 magrittr_2.0.3
## [73] data.table_1.14.4 reprex_2.0.2 googledrive_2.0.0
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## [79] patchwork_1.1.2 evaluate_0.18 xtable_1.8-4
## [82] HDO.db_0.99.1 XML_3.99-0.13 readxl_1.4.1
## [85] gridExtra_2.3 compiler_4.2.2 crayon_1.5.2
## [88] shadowtext_0.1.2 htmltools_0.5.3 ggfun_0.0.9
## [91] tzdb_0.3.0 snow_0.4-4 geneplotter_1.76.0
## [94] aplot_0.1.9 lubridate_1.9.0 DBI_1.1.3
## [97] tweenr_2.0.2 dbplyr_2.2.1 MASS_7.3-58.1
## [100] rappdirs_0.3.3 babelgene_22.9 Matrix_1.5-1
## [103] cli_3.4.1 parallel_4.2.2 igraph_1.3.5
## [106] pkgconfig_2.0.3 xml2_1.3.3 ggtree_3.6.2
## [109] svglite_2.1.1 annotate_1.76.0 bslib_0.4.1
## [112] XVector_0.38.0 rvest_1.0.3 yulab.utils_0.0.6
## [115] digest_0.6.30 Biostrings_2.66.0 rmarkdown_2.18
## [118] cellranger_1.1.0 fastmatch_1.1-3 tidytree_0.4.2
## [121] curl_4.3.3 lifecycle_1.0.3 nlme_3.1-160
## [124] jsonlite_1.8.3 viridisLite_0.4.1 limma_3.54.0
## [127] fansi_1.0.3 pillar_1.8.1 lattice_0.20-45
## [130] KEGGREST_1.38.0 fastmap_1.1.0 httr_1.4.4
## [133] GO.db_3.16.0 glue_1.6.2 png_0.1-7
## [136] bit_4.0.4 ggforce_0.4.1 stringi_1.7.8
## [139] sass_0.4.2 blob_1.2.3 textshaping_0.3.6
## [142] memoise_2.0.1 ape_5.6-2